NAME

       Bio::Tools::isPcr - Parse isPcr output and make features

SYNOPSIS

           # A simple annotation pipeline wrapper for isPcr data
           # assuming isPcr data is already generated in file seq1.isPcr
           # and sequence data is in fasta format in file called seq1.fa

           # Note: this parser is meant for the default fasta output from
           # isPcr.  bed and psl output formats are not supported.

           use Bio::Tools::IsPcr;
           use Bio::SeqIO;
           my $parser = Bio::Tools::isPcr->new(-file => 'seq1.isPcr');
           my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa');
           my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");

           while( my $feat = $parser->next_feature ) {
               # add isPcr annotation to a sequence
               $seq->add_SeqFeature($feat);
           }
           my $seqout = Bio::SeqIO->new(-format => 'embl');
           $seqout->write_seq($seq);

DESCRIPTION

       This object serves as a parser for isPcr data (in the default fasta format), creating a
       Bio::SeqFeatureI for each isPcr hit.  These can be processed or added as annotation to an
       existing Bio::SeqI object for the purposes of automated annotation.

       This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich
       (jason-at-bioperl.org).

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Sheldon McKay

       Email mckays@cshl.edu

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $ispcr = Bio::Tools::isPcr->new( -file => $file,
                                                     -primary => $fprimary,
                                                     -source => $fsource,
                                                     -groupclass => $fgroupclass);

        Function: Initializes a new isPcr parser
        Returns : Bio::Tools::isPcr
        Args    : -fh   => filehandle
                  OR
                  -file => filename

                  -primary => a string to be used as the common value for
                              each features '-primary' tag.  Defaults to
                              the sequence ontology term 'PCR_product'.
                              (This in turn maps to the GFF 'type'
                              tag (aka 'method')).

                   -source => a string to be used as the common value for
                              each features '-source' tag.  Defaults to
                              'isPcr'. (This in turn maps to the GFF 'source'
                              tag)

                   -groupclass => a string to be used as the name of the tag
                                  which will hold the sts marker namefirst
                                  attribute.  Defaults to 'name'.

   next_feature
        Title   : next_feature
        Usage   : $seqfeature = $obj->next_feature();
        Function: Returns the next feature available in the analysis result, or
                  undef if there are no more features.
        Example :
        Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
                  more features.
        Args    : none

   source
        Title   : source
        Usage   : $obj->source($newval)
        Function:
        Example :
        Returns : value of source (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   primary
        Title   : primary
        Usage   : $obj->primary($newval)
        Function:
        Example :
        Returns : value of primary (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   groupclass
        Title   : groupclass
        Usage   : $obj->groupclass($newval)
        Function:
        Example :
        Returns : value of groupclass (a scalar)
        Args    : on set, new value (a scalar or undef, optional)